Premier Daniel Andrews says some families will not the able to return to their homes for "extended periods of time" as the Commonwealth prepares to reopen a COVID-19 quarantine facility for displaced residents.

Late on Sunday emergency flood warnings were issued for the Campaspe River from Lake Eppalock to Rochester, and Fairy Dell, Kanyapella South, Koyuga and Nanneella.

The river at Echuca was peaking with major flooding higher than in January 2011, emergency authorities said.

Residents from Lake Eppalock to Barnadown, and Barnadown to Elmore were ordered to leave if safe to do so. It was too late for those living between Elmore and Rochester, who were advised to take shelter.

Those in Fairy Dell, Kanyapella South, Koyuga and Nanneella were told to seek higher ground.

Earlier emergency authorities ordered residents in Charlton and Echuca to leave their homes immediately, where up to 400 properties could be affected.

Residents in Shepparton, Orrvale, Murchison and Mooroopna were told it was too late to leave their communities.

Stephanie Turpin said the water rose fast overnight and her home in Shepparton's south was surrounded by water but not inundated.

"We're fairly high and fairly safe," she told AAP on Sunday.

Ms Turpin said police advised residents to leave on Saturday and again early on Sunday but she decided to stay and defend her property.

"There is no way of leaving now," she said.

"The community is sticking together and helping each other out. People are offering sandbags to other people around the neighbourhood."

She said some of the water was fast-flowing and dozens of homes and cars were flooded.

"But people are making the most of it. They've got canoes and floaties out. It doesn't happen very often."

Victorian State Emergency Service says more than 7300 homes and businesses in the Shepparton area could be affected by the rising waters, with inundation possible in about 2500 of those.

There were 146 flood rescues in the past 24 hours, with the majority in the Shepparton area, the SES said.

Prime Minister Anthony Albanese toured flood-affected areas with Premier Andrews, where about 9000 people are estimated to be affected.

Disaster recovery payments will be made available to residents in 23 local government areas and a 250-bed camp for displaced people will be opened at the former quarantine facility in Mickleham.

About 100 ADF personnel are also on their way to help with evacuations and sandbagging in the worst-hit area.

"We are working across federal, state and local government to make sure that every support is being provided to these communities that are under such enormous pressure," Mr Albanese told reporters.

"Australians are coming together, they are helping each other and once again we are seeing at the worst of times, the best of the Australian character."

Shepparton has been hit by major flooding, with the swollen Goulburn River expected to continue to rise through Sunday before peaking at 12.2 metres early on Monday.

That was higher than the 1974 flood level of 12.09m, the Bureau of Meteorology said.

Television footage showed buildings in the middle of town surrounded by a vast inland sea of brown water, and residents using sandbags to stop it.

Premier Andrews said the flooding was unlike other flooding events because high rainfall had left catchment areas sodden and more rain was forecast.

"These (river) peaks, even once they recede off the high mark, there will still be water in the communities and houses will remain uninhabitable for extended periods of time," he said.

Major flooding has peaked at Murchison, where the Goulburn peaked at 12m.

It has also hit communities along the Avoca River to Charlton, where the rising waterway had swollen to 7.73m on Sunday morning.

The river at Charlton could peak at 8m early on Monday.

The Wimmera River is also swollen, with Horsham residents warned major flooding was possible on Monday and into Tuesday.

Major flood warnings are also in place for the Broken, Avoca and Loddon rivers, and the Seven and Castle creeks.

Kerang residents have been advised to relocate or face being isolated for at least a week.

Echuca is expected to be hit by two flood peaks, one by Tuesday and another later in the week.

More than 350 roads are estimated to remain closed in flood-affected areas and about 6000 properties are without power.

Australian Associated Press